There is great need for new therapies for Duchenne Muscular Dystrophy (DMD), a currently incurable degenerative muscle disorder that affects 1 in every 3500 male births. Promising options include the transplantation of normal or gene-corrected muscle progenitors, which could engraft affected muscle fibers to correct the underlying genetic defects, as well as small molecule based therapies that could correct disrupted myogenic processes to support improved muscle function. Unfortunately, the rarity of regenerative muscle precursor cells and lack of relevant models that strongly mimic the progression and severity of human DMD has created many obstacles to understanding disease mechanisms and hindered the development of curative therapies. However, we believe that new innovations in epigenomic analysis and muscle stem cell biology, developed in part in our laboratories, have created new opportunities to discover and advance novel therapies in DMD. This project will exploit the combined expertise of the Wagers and Rinn research groups, which share common laboratory space in the Department of Stem Cell and Regenerative Biology at Harvard University. Studies in the Wagers lab have established novel strategies to isolate highly enriched populations of skeletal muscle progenitors (satellite cells) from human muscle and to derive engraftable myogenic precursor cells from human induced pluripotent stem cells. Studies in the Rinn lab have defined novel computational pipelines for the annotation and analysis of gene regulatory elements that specify cell fate and function. This project will combine these innovative advances with the unique resources provided by the NIH Epigenomics Roadmap Program to identify epigenetic regulators that drive human muscle progenitor cell identity and pinpoint those that may play a role in initiating or promoting DMD pathology. Our analyses will concentrate particularly on regulatory enhancers (e.g., Stretch or Super Enhancers, SEs), which represent regulatory hubs that frequently interact with the epigenetic and transcriptional machinery to control gene expression. We will use ChIP-Seq and transcriptional datasets to define muscle progenitor-specific SEs and their target genes, including candidate master transcriptional regulators of the muscle progenitor fate. Regulatory SEs and their targets will also be defined in skeletal muscle progenitors and terminal muscle cells derived from healthy or DMD patient induced pluripotent stem cells (iPSCs), using isogenic iPSC lines and novel culture-based strategies for generating and identifying myogenic precursors and their progeny at distinct stages of muscle differentiation. Together, this work will define the core regulatory and transcriptional landscapes that uniquely enforce the skeletal muscle progenitor cell fate, identify DMD-related alterations in enhancer activity that may drive disease progression, and further the application of iPSC-based technologies for the discovery of novel therapies for DMD and other muscle disorders.